Bottom Line:
The pentameric core domain, a doughnut-like structure with a central pore, is only found in the nucleoplasmin family.Furthermore, we show that two other chromatin proteins, Arabidopsis thaliana histone deacetylase type 2 (HD2) and Saccharomyces cerevisiae Fpr4, share the NPL fold and form pentamers, or a dimer of pentamers in the case of HD2.Thus, we propose a new family of proteins that share the pentameric nucleoplasmin-like NPL domain and are found in protists, fungi, plants and animals.

f0025: The structure of the FKBP39 NPL domain. (a) Superposition of 20 water-refined structures from the ensemble calculated from the final set of restraints. A 5-fold symmetry was enforced with non-crystallographic symmetry. (b) Cartoon representation of a monomer from the FKBP39 NPL structure (pink) superimposed with that from nucleoplasmin (1K5J, light green). The position of all β-strands is almost identical. (c) Electrostatic surface potential (− 60 to + 60 kT) viewed from the “top”, where the central pore is widest [same orientation as (a)]. (d) Side view of the same surface potential. The charges are quite evenly distributed over the surface.

Mentions:
Although the overall particle is large by NMR standards (54 kDa), it was possible to record good-quality 2D 1H-15N heteronuclear single quantum coherence (HSQC) spectra at ambient temperature. This encouraged us to determine the structure by NMR. With the aid of several isotope labelled samples, the structure of the NPL domain was determined. The ensemble of 20 water-refined structures is shown in Fig. 4a (structural statistics can be found in Supplementary Table 2). Solving the structure proved difficult because a mixed sample from proteins that had been isotope labelled in different ways was needed to assign inter-subunit nuclear Overhauser enhancements (NOEs), and it was not possible to reconstitute this due to the high stability of the NPL pentamer. This made it hard, and in some cases impossible, to assign inter-domain contacts (NOEs) close to the symmetry axis. For example, Ile56 contacts symmetry-related Ile56 residues in other subunits at the “bottom” of the central pore. Unambiguous assignment of a critical mass of inter-domain NOEs was eventually made with the aid of a deuterated sample that was selectively protonated on certain methyl groups and aromatic six-membered rings [16,17]. Once subunit contacts and the overall fold were determined, NOEs from other partially and fully protonated samples could be included to improve the structure.

f0025: The structure of the FKBP39 NPL domain. (a) Superposition of 20 water-refined structures from the ensemble calculated from the final set of restraints. A 5-fold symmetry was enforced with non-crystallographic symmetry. (b) Cartoon representation of a monomer from the FKBP39 NPL structure (pink) superimposed with that from nucleoplasmin (1K5J, light green). The position of all β-strands is almost identical. (c) Electrostatic surface potential (− 60 to + 60 kT) viewed from the “top”, where the central pore is widest [same orientation as (a)]. (d) Side view of the same surface potential. The charges are quite evenly distributed over the surface.

Mentions:
Although the overall particle is large by NMR standards (54 kDa), it was possible to record good-quality 2D 1H-15N heteronuclear single quantum coherence (HSQC) spectra at ambient temperature. This encouraged us to determine the structure by NMR. With the aid of several isotope labelled samples, the structure of the NPL domain was determined. The ensemble of 20 water-refined structures is shown in Fig. 4a (structural statistics can be found in Supplementary Table 2). Solving the structure proved difficult because a mixed sample from proteins that had been isotope labelled in different ways was needed to assign inter-subunit nuclear Overhauser enhancements (NOEs), and it was not possible to reconstitute this due to the high stability of the NPL pentamer. This made it hard, and in some cases impossible, to assign inter-domain contacts (NOEs) close to the symmetry axis. For example, Ile56 contacts symmetry-related Ile56 residues in other subunits at the “bottom” of the central pore. Unambiguous assignment of a critical mass of inter-domain NOEs was eventually made with the aid of a deuterated sample that was selectively protonated on certain methyl groups and aromatic six-membered rings [16,17]. Once subunit contacts and the overall fold were determined, NOEs from other partially and fully protonated samples could be included to improve the structure.

Bottom Line:
The pentameric core domain, a doughnut-like structure with a central pore, is only found in the nucleoplasmin family.Furthermore, we show that two other chromatin proteins, Arabidopsis thaliana histone deacetylase type 2 (HD2) and Saccharomyces cerevisiae Fpr4, share the NPL fold and form pentamers, or a dimer of pentamers in the case of HD2.Thus, we propose a new family of proteins that share the pentameric nucleoplasmin-like NPL domain and are found in protists, fungi, plants and animals.